rs9325854

Variant names:

• chr8-19293628-G-A
• rs9325854
• ENST00000777385.1:n.310-14628G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-19293628-G-A
• chr8-19293628-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000777385.1(ENSG00000301252):​n.310-14628G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0816 in 152,124 control chromosomes in the GnomAD database, including 947 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.082 (947 hom., cov: 32)
• Consequence: ENSG00000301252 ENST00000777385.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 3 publications found

Genes affected

ENSG00000301252 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301252	ENST00000777385.1	n.310-14628G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12399 AN: 152006 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0518

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.0772

Gnomad FIN AF: 0.0198

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0338

Gnomad OTH AF: 0.0632

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0816 AC: 12413 AN: 152124 Hom.: 947 Cov.: 32 AF XY: 0.0808 AC XY: 6011 AN XY: 74386

African (AFR) AF: 0.197 AC: 8175 AN: 41470

American (AMR) AF: 0.0516 AC: 789 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3470

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5164

South Asian (SAS) AF: 0.0775 AC: 372 AN: 4802

European-Finnish (FIN) AF: 0.0198 AC: 210 AN: 10608

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0339 AC: 2302 AN: 68002

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0491 Hom.: 532

Bravo AF: 0.0894

Asia WGS AF: 0.0530 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.53
PhyloP100		-0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9325854; hg19: chr8-19151139;